GigaPan megapixel imaging and best practices for digitizing entomological collections
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GigaPan megapixel imaging and best practices for digitizing entomological collections

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Katja C. Seltmann*1, Babi Hammond*2, Matthew Bertone1, Andrew R. Deans1 ...

Katja C. Seltmann*1, Babi Hammond*2, Matthew Bertone1, Andrew R. Deans1

1North Carolina State University, Department of Entomology, Campus

Box 7613, Raleigh, NC, USA;

2Department of Information Science, University of North Carolina, Chapel Hill, NC, USA



The North Carolina State {University} Insect Museum is working to image every drawer in the 1.5 million specimen collection and disseminate these data through the Web. The effort is worthwhile in that we expose the "research only" collection to the public, allow for remote curation of specimens, and enable more informed loan requests. The details and process for creating GigaPan (zoomable, mega-pixel images of entire drawers of specimens) images are outlined in the talk. Secondly, as part of a CollectionsWeb Research Coordination Network (RCN) funded internship awarded to Babi Hammond, preliminary results of a survey is presented looking at the use of online entomological collection data. Survey participants are asked to review and rate the utility of multiple online presentations of collection data; specimen information without images, GigaPan images, and detailed images with specimen data. The results will help institutions with entomological collections and the Advancing Digitization of Biological Collections (ADBC) program participants better understand how to apply their resources and digitization efforts.

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  • From meeting with ALA; similar to SatScan but less expensive;
  • Did not develop anything; used existing technology and streamlined workflow
  • Includes specimen staging; cost of hourly wage earners; many of the kinks worked out now
  • Used presently existing technology and consentrated on workflow
  • We are not very good at marketing our own stuff; Existing Website makes it a challenge to give us feedback from annotations; Search mechanisms not granular enough for collection information; need better annotation tool - perhaps the ability to annotate phenotypes?
  • Mark Greene and Dennis Meissner American Archivist 68 (2005): 208-263 movement in archival processing that deals with the realization that we will not be able to be 100perfect, so it is important to identify where we can get the most inforamtion for minimal effort
  • Kevin Williams found misidentified (outdated identification) in Mutillidae; Determinations of cercopids by Andy Hamelton; Collection even examined by an individual in order to make an informed donations; inclusion of expansion space (curation of collection); seen as 10 year event Transisiton into benchmarking efforts
  • 2,200 individual images to create this GigaPan
  • Alex Smith fine fellows grant; found habitat and linked 2; not anticipated
  • 1.6 million specimens NSF BRC grant for collection improvement NO PUBLIC COLLECTION
  • Babi Collectionweb Don’t worry about it saying entomologist
  • Small taxon authority databases presently most used

Transcript

  • 1. GigaPan megapixel imaging and best practices for digitizing entomological collections NCSU Insect Museum, North Carolina State University Metadata Research Center/SILS/University North Carolina, Chapel Hill NC STATE UNIVERSITY Entomological Collections Network Meeting Reno, 2011 Katja Seltmann, Babi Hammond, Matthew Bertone, Jane Greenberg, and Andrew R. Deans
  • 2. [Outline]
    • Part 1: Whole drawer imaging & GigaPan at NCSU Insect Museum
    • Part 2: Benchmarking Efforts
  • 3. [NCSU Insect Museum]
    • Founded in 1952
    • Past/present researchers:
      • Historically: Z.P. Metcalf (Auchenorrhyncha), C.S. Brimley (NC insects), T.B. Mitchell (Anthophila), C.F. Smith (Aphididae), M.H. Farrier (Acari), D.A. Young (Auchenorrhyncha), H.H. Neunzig (Pyraloidea), L.L. Deitz (Auchenorrhyncha)
      • Currently: A.R. Deans (Hymenoptera) & B.M. Wiegmann (Diptera)
      • Head Curator: Bob Blinn
    • Currently one of the two largest insect collections in the Southeast US (~1.4 million)
  • 4. [The Concept]
    • A high-quality image for each drawer in the collection
      • “ Virtual Museum”
  • 5. [GigaPan]
    • Robot developed for Mars rover
      • NASA + CMU
    • Commercially = robot plus software
    • Robot takes multiple images using standard camera
    • Software stitches images
    • GigaPan website
    GigaPan Epic 100 with camera
  • 6. [GigaPan: Components]
    • OUR SETUP:
    • GigaPan Epic 100
    • Canon G11
    • Copy stand
    • Continuous fluorescent daylight lamps
    • Power supplies for GigaPan and Canon
    $450.00 $500.00 $100.00 $500.00 $100.00 ~$1,650.00 $1,000 http://www.gigapan.org/profiles/23796/
  • 7. [GigaPan: People]
    • Costs:
    • 10 minutes per GigaPan
    • $2 dollars a drawer
    • 2500 drawers
    ~$5,000 http://www.gigapan.org/profiles/23796/
  • 8.
    • <$10,000!
    • for 2,500 drawers
    • a great success
    [GigaPan: Total] http://www.gigapan.org/profiles/23796/
  • 9.  
  • 10. zoom tools panorama snapshots w/comments geo-reference explore score panorama info panorama comments
  • 11. [GigaPan: Methods]
    • http://blog.insectmuseum.org/?tag=gigapan
      • (Bertone & Deans)
  • 12.  
  • 13.  
  • 14.  
  • 15. [Results]
    • So far NCSU Insect Museum (ID 23796) has 1783 panoramas
      • Most panoramas of any user so far
      • Major effort began in June 2010
      • Expect to finish in the Spring
    • Panoramas average 0.2 gigapixels (200 mp)
    • http://www.gigapan.org/profiles/23796/
    • Remote annotation & increased interaction with the collection
    http://www.gigapan.org/profiles/23796/
  • 16. [Results]
    • Juried gallery winner
      • Fine Conference on Gigapixel Imaging
    • Work highlighted by:
      • Science Magazine
      • New Scientist
      • Wired
      • National Geographic
      • Others...
    • One Panorama has 23,292 views so far
    • 181,019 Total Views
  • 17. [Realized & Potential Issues]
    • Dynamic collection
    • Only one view of specimens*
    • Resolution of small specimens
    • Large specimens obscure labels*
    • Parallax/distortion
    • Accommodating larger drawers
    • Hosting & annotation capabilities limited using GigaPan website
    • Poor marketers
    *may not be alleviated by any system Issues are all future opportunities
  • 18. [Realized & Potential Outcomes]
    • Remote identification
    • Curatorial advice*
    • Non-expert/public engagement
    • Better informed donations*
    • Better informed requests
    • Megapixel imaging for other purposes
      • Linking of specimens to habitat panoramas*
      • Micro images & remote taxonomy
    *unanticipated Outcomes are all future opportunities
  • 19.  
  • 20. “ Lots of hairs” “ Not much here (a bit abstract)”
  • 21. Panorama by Alex Smith (University of Guelph)
  • 22. [Part 2: Benchmarks]
    • We have some ideas.. might even call them hypotheses… are we right?
    • Utility of whole drawer imaging of collections in contrast with other methods?
    • Most used websites?
    • What online collection data is deemed useful?
    • Who finds online images and collection data useful?
  • 23. [ information science ]
    • No way of knowing if what we are doing is successful unless we benchmark and test that success
    • Define best practices by first discovering how the community actual uses collections
    • Partnered with Babi Hammond at UNC, Chapel Hill
      • CollectionsWeb RCN
      • Developed a survey to establish these benchmarks
    • http://tinyurl.com/625xeb9
    6 … 2 … 5 … xeb ...9
  • 24. [Help!]
    • Promoting our survey to help us determine present best practices for digitizing entomological collections
    • http://tinyurl.com/625xeb9
    6 … 2 … 5 … xeb ...9
  • 25. [preliminary results]
    • 90 participants
    • Majority taxonomists
    • Primarily faculty with PhD
    • Need help reaching a wider audience
      • Looking for entomologists worldwide
      • Please help by sending survey through internal lists
  • 26. [benchmark]
    • “ Which online presentations are successful?”
  • 27. [benchmark] (results so far: tiny significance)
  • 28.
    • “ Which online presentations are successful?”
    [follow up action?]
  • 29. [benchmark survey]
    • Finish survey in the Spring
      • Babi’s thesis work will be published
    • Want more participants
    • Need to make it a habit to include the science of information in our future projects; inexpensive to include them
    6 … 2 … 5 … xeb ...9
  • 30. [Acknowledgments]
    • National Science Foundation DBI-0847924
    • CollectionsWeb RCN
    • Metadata Research Center
    • /SILS/University of North
    • Carolina, Chapel Hill
    • Istvan Miko, & Matthew Yoder
    • Kelly Dew, Tanner Stanfield,
    • Lydia Abernethy, & Bob Blinn
    • Mary Jo Daines (CREATE)
    • Randy Sargent (NASA-Ames)
    • Steve Denning (NCSU)
    • GigaPan Community
    • http://tinyurl.com/625xeb9
    • http://www.gigapan.org/profiles/23796/
    NC STATE UNIVERSITY